data_2UKD # _model_server_result.job_id KrOr7hWPxomRx0HB6zRCZg _model_server_result.datetime_utc '2024-10-18 23:29:36' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2ukd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":195}' # _entry.id 2UKD # _exptl.entry_id 2UKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 2UKD _cell.length_a 78.7 _cell.length_b 78.7 _cell.length_c 100.1 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2UKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 C O2B ADP . A ADP 195 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc2 E O HOH . A HOH 198 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc3 E O HOH . A HOH 215 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc4 E O HOH . A HOH 220 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc5 E O HOH . A HOH 227 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc6 B MG MG . A MG 500 1_555 E O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 2UKD _atom_sites.fract_transf_matrix[1][1] 0.012706 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012706 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.00999 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 MG A 1 500 500 MG MG . C 3 ADP A 1 195 195 ADP ADP . D 4 C5P A 1 196 196 C5P C5P . E 5 HOH A 1 197 197 HOH HOH . E 5 HOH A 2 198 198 HOH HOH . E 5 HOH A 3 200 200 HOH HOH . E 5 HOH A 4 201 201 HOH HOH . E 5 HOH A 5 202 202 HOH HOH . E 5 HOH A 6 203 203 HOH HOH . E 5 HOH A 7 204 204 HOH HOH . E 5 HOH A 8 206 206 HOH HOH . E 5 HOH A 9 207 207 HOH HOH . E 5 HOH A 10 208 208 HOH HOH . E 5 HOH A 11 209 209 HOH HOH . E 5 HOH A 12 210 210 HOH HOH . E 5 HOH A 13 211 211 HOH HOH . E 5 HOH A 14 212 212 HOH HOH . E 5 HOH A 15 214 214 HOH HOH . E 5 HOH A 16 215 215 HOH HOH . E 5 HOH A 17 216 216 HOH HOH . E 5 HOH A 18 218 218 HOH HOH . E 5 HOH A 19 220 220 HOH HOH . E 5 HOH A 20 221 221 HOH HOH . E 5 HOH A 21 222 222 HOH HOH . E 5 HOH A 22 223 223 HOH HOH . E 5 HOH A 23 226 226 HOH HOH . E 5 HOH A 24 227 227 HOH HOH . E 5 HOH A 25 228 228 HOH HOH . E 5 HOH A 26 229 229 HOH HOH . E 5 HOH A 27 231 231 HOH HOH . E 5 HOH A 28 232 232 HOH HOH . E 5 HOH A 29 233 233 HOH HOH . E 5 HOH A 30 234 234 HOH HOH . E 5 HOH A 31 236 236 HOH HOH . E 5 HOH A 32 238 238 HOH HOH . E 5 HOH A 33 239 239 HOH HOH . E 5 HOH A 34 242 242 HOH HOH . E 5 HOH A 35 244 244 HOH HOH . E 5 HOH A 36 245 245 HOH HOH . E 5 HOH A 37 501 501 HOH HOH . E 5 HOH A 38 509 509 HOH HOH . E 5 HOH A 39 512 512 HOH HOH . E 5 HOH A 40 528 528 HOH HOH . E 5 HOH A 41 531 531 HOH HOH . E 5 HOH A 42 532 532 HOH HOH . E 5 HOH A 43 533 533 HOH HOH . E 5 HOH A 44 536 536 HOH HOH . E 5 HOH A 45 538 538 HOH HOH . E 5 HOH A 46 543 543 HOH HOH . E 5 HOH A 47 553 553 HOH HOH . E 5 HOH A 48 558 558 HOH HOH . E 5 HOH A 49 559 559 HOH HOH . E 5 HOH A 50 562 562 HOH HOH . E 5 HOH A 51 563 563 HOH HOH . E 5 HOH A 52 564 564 HOH HOH . E 5 HOH A 53 565 565 HOH HOH . E 5 HOH A 54 566 566 HOH HOH . E 5 HOH A 55 568 568 HOH HOH . E 5 HOH A 56 569 569 HOH HOH . E 5 HOH A 57 577 577 HOH HOH . E 5 HOH A 58 580 580 HOH HOH . E 5 HOH A 59 582 582 HOH HOH . E 5 HOH A 60 591 591 HOH HOH . E 5 HOH A 61 597 597 HOH HOH . E 5 HOH A 62 601 601 HOH HOH . E 5 HOH A 63 602 602 HOH HOH . E 5 HOH A 64 603 603 HOH HOH . E 5 HOH A 65 604 604 HOH HOH . E 5 HOH A 66 605 605 HOH HOH . E 5 HOH A 67 608 608 HOH HOH . E 5 HOH A 68 616 616 HOH HOH . E 5 HOH A 69 640 640 HOH HOH . E 5 HOH A 70 650 650 HOH HOH . E 5 HOH A 71 664 664 HOH HOH . E 5 HOH A 72 670 670 HOH HOH . E 5 HOH A 73 717 717 HOH HOH . E 5 HOH A 74 727 727 HOH HOH . E 5 HOH A 75 732 732 HOH HOH . E 5 HOH A 76 737 737 HOH HOH . E 5 HOH A 77 739 739 HOH HOH . E 5 HOH A 78 741 741 HOH HOH . E 5 HOH A 79 744 744 HOH HOH . E 5 HOH A 80 746 746 HOH HOH . E 5 HOH A 81 747 747 HOH HOH . E 5 HOH A 82 750 750 HOH HOH . E 5 HOH A 83 751 751 HOH HOH . E 5 HOH A 84 752 752 HOH HOH . E 5 HOH A 85 753 753 HOH HOH . E 5 HOH A 86 767 767 HOH HOH . E 5 HOH A 87 769 769 HOH HOH . E 5 HOH A 88 774 774 HOH HOH . E 5 HOH A 89 778 778 HOH HOH . E 5 HOH A 90 779 779 HOH HOH . E 5 HOH A 91 781 781 HOH HOH . E 5 HOH A 92 786 786 HOH HOH . E 5 HOH A 93 797 797 HOH HOH . E 5 HOH A 94 801 801 HOH HOH . E 5 HOH A 95 807 807 HOH HOH . E 5 HOH A 96 810 810 HOH HOH . E 5 HOH A 97 816 816 HOH HOH . E 5 HOH A 98 818 818 HOH HOH . E 5 HOH A 99 819 819 HOH HOH . E 5 HOH A 100 823 823 HOH HOH . E 5 HOH A 101 824 824 HOH HOH . E 5 HOH A 102 825 825 HOH HOH . E 5 HOH A 103 826 826 HOH HOH . E 5 HOH A 104 827 827 HOH HOH . E 5 HOH A 105 828 828 HOH HOH . E 5 HOH A 106 829 829 HOH HOH . E 5 HOH A 107 832 832 HOH HOH . E 5 HOH A 108 833 833 HOH HOH . E 5 HOH A 109 837 837 HOH HOH . E 5 HOH A 110 838 838 HOH HOH . E 5 HOH A 111 839 839 HOH HOH . E 5 HOH A 112 840 840 HOH HOH . E 5 HOH A 113 843 843 HOH HOH . E 5 HOH A 114 844 844 HOH HOH . E 5 HOH A 115 845 845 HOH HOH . E 5 HOH A 116 848 848 HOH HOH . E 5 HOH A 117 849 849 HOH HOH . E 5 HOH A 118 853 853 HOH HOH . E 5 HOH A 119 857 857 HOH HOH . E 5 HOH A 120 863 863 HOH HOH . E 5 HOH A 121 864 864 HOH HOH . E 5 HOH A 122 870 870 HOH HOH . E 5 HOH A 123 871 871 HOH HOH . E 5 HOH A 124 872 872 HOH HOH . E 5 HOH A 125 874 874 HOH HOH . E 5 HOH A 126 877 877 HOH HOH . E 5 HOH A 127 879 879 HOH HOH . E 5 HOH A 128 881 881 HOH HOH . E 5 HOH A 129 882 882 HOH HOH . E 5 HOH A 130 883 883 HOH HOH . E 5 HOH A 131 890 890 HOH HOH . E 5 HOH A 132 900 900 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB ADP . . . C 3 38.301 65.623 -11.837 1 17.75 ? PB ADP 195 A 1 HETATM 2 O O1B ADP . . . C 3 38.779 64.591 -12.737 1 18.15 ? O1B ADP 195 A 1 HETATM 3 O O2B ADP . . . C 3 39.309 66.505 -11.308 1 19.8 ? O2B ADP 195 A 1 HETATM 4 O O3B ADP . . . C 3 37.213 66.5 -12.551 1 17.31 ? O3B ADP 195 A 1 HETATM 5 P PA ADP . . . C 3 37.522 65.021 -9.029 1 18.48 ? PA ADP 195 A 1 HETATM 6 O O1A ADP . . . C 3 38.73 64.44 -8.51 1 18.56 ? O1A ADP 195 A 1 HETATM 7 O O2A ADP . . . C 3 37.256 66.401 -8.658 1 17.64 ? O2A ADP 195 A 1 HETATM 8 O O3A ADP . . . C 3 37.558 64.933 -10.627 1 19.24 ? O3A ADP 195 A 1 HETATM 9 O O5' ADP . . . C 3 36.298 64.122 -8.597 1 20.78 ? O5' ADP 195 A 1 HETATM 10 C C5' ADP . . . C 3 34.937 64.32 -9.082 1 19.78 ? C5' ADP 195 A 1 HETATM 11 C C4' ADP . . . C 3 33.91 63.839 -8.016 1 21.17 ? C4' ADP 195 A 1 HETATM 12 O O4' ADP . . . C 3 33.953 62.412 -8.053 1 19.65 ? O4' ADP 195 A 1 HETATM 13 C C3' ADP . . . C 3 34.208 64.322 -6.59 1 20.06 ? C3' ADP 195 A 1 HETATM 14 O O3' ADP . . . C 3 33.048 64.564 -5.873 1 22.42 ? O3' ADP 195 A 1 HETATM 15 C C2' ADP . . . C 3 34.885 63.104 -6.067 1 20.58 ? C2' ADP 195 A 1 HETATM 16 O O2' ADP . . . C 3 34.738 63.041 -4.672 1 22.14 ? O2' ADP 195 A 1 HETATM 17 C C1' ADP . . . C 3 34.155 61.944 -6.752 1 20 ? C1' ADP 195 A 1 HETATM 18 N N9 ADP . . . C 3 34.987 60.777 -6.951 1 20.02 ? N9 ADP 195 A 1 HETATM 19 C C8 ADP . . . C 3 36.283 60.705 -7.429 1 19.77 ? C8 ADP 195 A 1 HETATM 20 N N7 ADP . . . C 3 36.679 59.523 -7.709 1 19.55 ? N7 ADP 195 A 1 HETATM 21 C C5 ADP . . . C 3 35.617 58.744 -7.359 1 20.32 ? C5 ADP 195 A 1 HETATM 22 C C6 ADP . . . C 3 35.445 57.361 -7.423 1 20.74 ? C6 ADP 195 A 1 HETATM 23 N N6 ADP . . . C 3 36.474 56.481 -7.704 1 19.86 ? N6 ADP 195 A 1 HETATM 24 N N1 ADP . . . C 3 34.211 56.874 -7.11 1 22.38 ? N1 ADP 195 A 1 HETATM 25 C C2 ADP . . . C 3 33.261 57.76 -6.723 1 21.06 ? C2 ADP 195 A 1 HETATM 26 N N3 ADP . . . C 3 33.405 59.065 -6.499 1 20.67 ? N3 ADP 195 A 1 HETATM 27 C C4 ADP . . . C 3 34.59 59.497 -6.887 1 19.57 ? C4 ADP 195 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 27 #